Align Phosphotransferase system IIB component, component of Fructose-specific Enzyme I-HPr-Enzyme IIABC complex, all encoded within a single operon with genes in the order: ptsC (IIC), ptsA (IIA), ptsH (HPr), ptsI (Enzyme I) and ptsB (IIB) (characterized)
to candidate WP_072908771.1 BUB13_RS10825 PTS fructose-like transporter subunit IIB
Query= TCDB::Q5V5X1 (143 letters) >NCBI__GCF_900142125.1:WP_072908771.1 Length = 575 Score = 108 bits (269), Expect = 2e-28 Identities = 58/117 (49%), Positives = 80/117 (68%), Gaps = 1/117 (0%) Query: 3 LVAVTSCPTGIAHSQMAAENLEQTAEEQGHDIKVEVQGAMGAENELSDSDIEAADAAIIA 62 +V VTSCPTGIAH+ MAAE L++ AEE GH++K+E QG++GA+N LSD +I ADA IIA Sbjct: 118 IVGVTSCPTGIAHTFMAAEALKKAAEELGHEVKIETQGSVGAKNVLSDDEIARADAVIIA 177 Query: 63 SDTSVSQDRFSGVPLIDGTVKDAVNDAEGMIADAVKAADGDTP-ARETDVGSSEASA 118 +D V + RFSG PL + + K+A+++ I A+ AA A++ D SE SA Sbjct: 178 ADAFVDKTRFSGKPLFETSTKEALHNGANAIQAALSAAPAAKGLAKQVDDLKSERSA 234 Score = 81.6 bits (200), Expect = 2e-20 Identities = 41/99 (41%), Positives = 63/99 (63%) Query: 2 KLVAVTSCPTGIAHSQMAAENLEQTAEEQGHDIKVEVQGAMGAENELSDSDIEAADAAII 61 K+VAVT+CPTG+AH+ MAAE L++ A+ GH++++E QG+ GA++ L+ I AD II Sbjct: 3 KIVAVTACPTGVAHTFMAAEALKKVADTMGHELELETQGSEGAKDVLAPDAIAQADVVII 62 Query: 62 ASDTSVSQDRFSGVPLIDGTVKDAVNDAEGMIADAVKAA 100 A+D V RF+G + + DA+ + +I A A Sbjct: 63 AADIHVDPSRFAGKAIHAVSTSDAIRQTKEVIEAAFAEA 101 Lambda K H 0.308 0.124 0.328 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 158 Number of extensions: 5 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 143 Length of database: 575 Length adjustment: 26 Effective length of query: 117 Effective length of database: 549 Effective search space: 64233 Effective search space used: 64233 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.7 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory